Open Research in TopoStats

Laura Wiggins, Sylvia Whittle

What is TopoStats?

  • Automated software for processing Atomic Force Microscopy images.
  • Takes in data, produces pretty pictures and useful stats.
  • Used for research into DNA, cancer and pharmaceuticals.

How we approach Open Research in TopoStats

FAIR4RS

TopoStats development has been guided by the FAIR4RS (FAIR 4 Research Software) principles.

  • Findable
  • Accessible
  • Interoperable
  • Reusable

Ease of installation

  • TopoStats is installable through PIP:
pip install topostats
  • Pre-release versions are installable via GitHub:
git clone https://github.com/AFM-SPM/TopoStats.git
cd TopoStats
pip install -e .

Open project management

  • Issues
  • Project feature board
  • Discussion Forums
  • Milestones
  • Code of Conduct
  • Bug & Feature templates

Docs, Versioning & Ease of use

  • Versioned releases
  • Automatic publishing to ORDA
  • Automatic API documentation
  • Easy to use config files
  • Jupyter Notebooks
  • Running courses & workshops

Development workflow

  • Python PEP-8
  • Auto-formatting with Black
  • Linting via Pylint & Flake8
  • Pre-commit to ensure adherence
  • Pre-commit CI on GitHub
  • Comprehensive testing
  • Constant refactoring & organisation

Acknowledgements

  • Tom Catley
  • Jean Du
  • Tobi Firth
  • Max Gamill
  • Libby Holmes
  • Rob Moorehead
  • Alice Pyne
  • Eddie Rollins
  • Neil Shephard
  • Billie Ward
  • Laura Wiggins
  • Sylvia Whittle